Short palate, lung and nasal epithelium clone 1 (SPLUNC1) gene coded a secreted protein found at the surface of nasopharyngeal epithelium, which may be an innate immunity defensive molecular and a risk factor for nasopharyngeal carcinoma (NPC). Here, we observed the effects of SPLUNC1 on the Gram negative bacteria Pseudomonas aeruginosa, evaluated the ability of SPLUNC1 protein binding to lipopolysaccharide. To observe the effect of SPLUNC1 protein on Epstein-Barr virus (EBV), we raised three EBV-transformed B-lymphocyte lines and treated the cells by SPLUNC1 protein; cellular disruption, apoptosis, EBV DNA content, and viral oncogene expression were analyzed. We found that SPLUNC1 protein can bind to bacterial lipopolysaccharide, inhibit the growth of P. aeruginosa, enhance the disruption and apoptosis of EBV-infected B-lymphocytes, downregulate protein expression of EBV latent membrane protein 1, while upregulate protein expression of EBV envelope glycoprotein gp350/220. The total EBV DNA in the culture medium was decreased significantly after 7 days of treatment by SPLUNC1. This study shows that SPLUNC1 not only has the role of antibacteria and antivirus, but also inhibits the potential oncogenicity of EBV in respiratory epithelium.